CHST14 p.Phe227=
c.681T>C · rs749932360 · VCV2963009
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
Ehlers-Danlos syndrome, musculocontractural type
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.5 | GERP -3.8 |
| Overall | ||
| CADD | 9.071 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- CHST14
- Protein
- p.Phe227=
- Coding
- c.681T>C
- MANE Select
- NM_130468
- dbSNP
- rs749932360
- Type
- single nucleotide variant
- Location
- chr15:40471894 (GRCh38)
- Gene constraint
- LOEUF 0.917 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.17
Disease context
Ehlers-Danlos syndrome, musculocontractural type — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Musculocontractural Ehlers-Danlos syndrome (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Infancy, Neonatal
Similar variants
- CHST14 p.Arg213Pro Likely pathogenic ★★ same condition
- CHST14 p.Arg320Ter Likely pathogenic ★★ same condition
- CHST14 p.Gln204Ter Pathogenic/Likely pathogenic ★★ same condition
- CHST14 p.Glu262Lys Pathogenic/Likely pathogenic ★★ same condition
- CHST14 p.Tyr293Cys Pathogenic/Likely pathogenic ★★ same condition
- CHST14 p.Ala11Val Uncertain significance ★★ ⚠ same condition
- CHST14 p.Ala15Pro Uncertain significance ★★ ⚠ same condition
- CHST14 p.Ala290Val Uncertain significance ★★ ⚠ same condition
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/chst14-p-phe227 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown